I compared the pin assignments, and the things that stick out to me aren't any differen't than what you've already said. C2 19 on the 2004 is an oil pressure switch input and not present on the 1998. I don't know if that is required for the engine to stay running, but it sounds like it won't even start in the first place.
One thing to consider is the MAP sensor. An L67 PCM expects to see a 2 bar MAP sensor. An L36 PCM expects to see a 1 bar MAP sensor. I once put an L67 PCM into an L36 car without changing the MAP sensor. I had purchased a 2 bar MAP sensor but I just forgot to swap it in. It would not start. Once I removed the 1 bar MAP sensor and replaced it with the 2 bar, it started right up.
It's possible that your tuning software never actually disabled VATS in your 2004 PCM. I know when I've done it, several values had to be changed and it was not intuitive at all, but I'm not familiar with the software you are using.
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